[2023-03-19 02:16:59,668] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:16:59,671] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:16:59,671] [INFO] DQC Reference Directory: /var/lib/cwl/stgd785e4c3-4418-4cee-8d40-1d9697294d87/dqc_reference
[2023-03-19 02:17:00,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:17:00,762] [INFO] Task started: Prodigal
[2023-03-19 02:17:00,762] [INFO] Running command: cat /var/lib/cwl/stg5abdc169-73c5-45a3-8dbb-7cbfd409f531/OceanDNA-b41706.fa | prodigal -d OceanDNA-b41706/cds.fna -a OceanDNA-b41706/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:17:05,267] [INFO] Task succeeded: Prodigal
[2023-03-19 02:17:05,267] [INFO] Task started: HMMsearch
[2023-03-19 02:17:05,267] [INFO] Running command: hmmsearch --tblout OceanDNA-b41706/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd785e4c3-4418-4cee-8d40-1d9697294d87/dqc_reference/reference_markers.hmm OceanDNA-b41706/protein.faa > /dev/null
[2023-03-19 02:17:05,430] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:17:05,431] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5abdc169-73c5-45a3-8dbb-7cbfd409f531/OceanDNA-b41706.fa]
[2023-03-19 02:17:05,438] [INFO] Query marker FASTA was written to OceanDNA-b41706/markers.fasta
[2023-03-19 02:17:05,439] [INFO] Task started: Blastn
[2023-03-19 02:17:05,439] [INFO] Running command: blastn -query OceanDNA-b41706/markers.fasta -db /var/lib/cwl/stgd785e4c3-4418-4cee-8d40-1d9697294d87/dqc_reference/reference_markers.fasta -out OceanDNA-b41706/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:17:05,873] [INFO] Task succeeded: Blastn
[2023-03-19 02:17:05,873] [INFO] Selected 12 target genomes.
[2023-03-19 02:17:05,874] [INFO] Target genome list was writen to OceanDNA-b41706/target_genomes.txt
[2023-03-19 02:17:05,878] [INFO] Task started: fastANI
[2023-03-19 02:17:05,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg5abdc169-73c5-45a3-8dbb-7cbfd409f531/OceanDNA-b41706.fa --refList OceanDNA-b41706/target_genomes.txt --output OceanDNA-b41706/fastani_result.tsv --threads 1
[2023-03-19 02:17:09,350] [INFO] Task succeeded: fastANI
[2023-03-19 02:17:09,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd785e4c3-4418-4cee-8d40-1d9697294d87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:17:09,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd785e4c3-4418-4cee-8d40-1d9697294d87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:17:09,350] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:17:09,350] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:17:09,351] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-19 02:17:09,451] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41706/tc_result.tsv
[2023-03-19 02:17:09,451] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:17:09,451] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:17:09,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd785e4c3-4418-4cee-8d40-1d9697294d87/dqc_reference/checkm_data
[2023-03-19 02:17:09,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:17:09,468] [INFO] Task started: CheckM
[2023-03-19 02:17:09,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41706/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41706/checkm_input OceanDNA-b41706/checkm_result
[2023-03-19 02:17:26,667] [INFO] Task succeeded: CheckM
[2023-03-19 02:17:26,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.87%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:17:26,677] [INFO] ===== Completeness check finished =====
[2023-03-19 02:17:26,677] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:17:26,677] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41706/markers.fasta)
[2023-03-19 02:17:26,678] [INFO] Task started: Blastn
[2023-03-19 02:17:26,678] [INFO] Running command: blastn -query OceanDNA-b41706/markers.fasta -db /var/lib/cwl/stgd785e4c3-4418-4cee-8d40-1d9697294d87/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41706/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:17:27,086] [INFO] Task succeeded: Blastn
[2023-03-19 02:17:27,097] [INFO] Selected 12 target genomes.
[2023-03-19 02:17:27,097] [INFO] Target genome list was writen to OceanDNA-b41706/target_genomes_gtdb.txt
[2023-03-19 02:17:27,135] [INFO] Task started: fastANI
[2023-03-19 02:17:27,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg5abdc169-73c5-45a3-8dbb-7cbfd409f531/OceanDNA-b41706.fa --refList OceanDNA-b41706/target_genomes_gtdb.txt --output OceanDNA-b41706/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:17:29,832] [INFO] Task succeeded: fastANI
[2023-03-19 02:17:29,840] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:17:29,840] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_003279605.1	s__MEDG-81 sp003279605	85.6399	257	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902561325.1	s__MEDG-81 sp902561325	85.1062	231	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	98.13	98.13	0.81	0.81	2	-
GCA_902514765.1	s__MEDG-81 sp902514765	84.9027	178	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213595.1	s__MEDG-81 sp003213595	84.7581	244	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	99.82	99.63	0.96	0.91	3	-
GCA_902514645.1	s__MEDG-81 sp902514645	84.5638	171	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902632605.1	s__MEDG-81 sp902632605	84.4977	232	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902587545.1	s__MEDG-81 sp902587545	84.4896	231	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625415.1	s__MEDG-81 sp902625415	84.4496	250	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595715.1	s__MEDG-81 sp902595715	84.4367	216	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902540995.1	s__MEDG-81 sp902540995	84.2658	196	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	98.42	98.42	0.80	0.80	2	-
GCA_902629465.1	s__MEDG-81 sp902629465	83.7735	173	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902627595.1	s__MEDG-81 sp902627595	83.3836	209	291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	97.00	97.00	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:17:29,841] [INFO] GTDB search result was written to OceanDNA-b41706/result_gtdb.tsv
[2023-03-19 02:17:29,841] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:17:29,842] [INFO] DFAST_QC result json was written to OceanDNA-b41706/dqc_result.json
[2023-03-19 02:17:29,842] [INFO] DFAST_QC completed!
[2023-03-19 02:17:29,842] [INFO] Total running time: 0h0m30s